\documentclass{article}

% -- Add this section to your LaTeX doc
% Remember to use "pdflatex -shell-escape myfile.tex"
% or it won't allow LaTeX to call any command-line
% programs!
\usepackage{graphicx}
\newcounter{smilescounter}
\setcounter{smilescounter}{1}
\newcommand{\smiles}[1]{
\immediate\write18{obabel -:"#1" -O smilesimg\arabic{smilescounter}.png}
\includegraphics{smilesimg\arabic{smilescounter}.png}
\addtocounter{smilescounter}{1}
}
% -- End of section

\title{This is an example of use}
\author{Noel O'Boyle}
\date{26 March 2012}
\begin{document}
   \maketitle
The following images were created using the smiles command.

\begin{figure}[h!]
  \smiles{CCO}
  \caption{Ethanol.}
  \centering
\end{figure}

\begin{figure}[h!]
  \smiles{[C@H]2(OC1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)CO)[C@H](O)[C@@H](O)C(O[C@@H]2CO)O[C@H]3[C@H](O)[C@@H](O)[C@H](O[C@@H]3CO)O}
  \caption{Not ethanol.}
  \centering
\end{figure}
\end{document}